: Occurrence in the Human Gut Microbiota and -Mer-Based Assessment of Intraspecies Diversity.

Alignment-free approaches employing short -mers as barcodes for individual genomes have created a new strategy for taxonomic analysis and paved a way for high-resolution phylogeny. Here, we introduce this strategy for the species as a taxon requiring barcoding support for precise systematics. Using this approach for phylotyping of VKM B-1144 at the genus level, we identified four phylogroups and found that 12A belongs to one of them, rather than to the clade. Therefore, we propose to change the specification of this strain. At the genus level we found only one relative of VKM B-1144 among 221 genomes, complete or available in contigs, and showed that the coding potential of the genome of this "rare" strain allows its consideration as a potential probiotic component. Four sets of published metagenomes were used to assess the dependence of presence in the human gut microbiome on chronic diseases, dietary changes and antibiotic treatment. Only antibiotics significantly affected their presence, and strain-specific barcoding allowed the identification of the main scenarios of the adaptive response. Thus, suggesting bacteria of this species for compensatory therapy, we also propose strain-specific barcoding for selecting optimal strains for target microbiomes.